NAME
gt-encseq-encode - Encode sequence files (FASTA/FASTQ, GenBank, EMBL) efficiently.
SYNOPSIS
gt encseq encode sequence_file [sequence_file [sequence_file …]]
DESCRIPTION
- -showstats [yes|no]
-
show compression results (default: no)
- -ssp [yes|no]
-
output sequence separator positions to file (default: yes)
- -des [yes|no]
-
output sequence descriptions to file (default: yes)
- -sds [yes|no]
-
output sequence description separator positions to file (default: yes)
- -md5 [yes|no]
-
output MD5 sums to file (default: yes)
- -clipdesc [yes|no]
-
clip descriptions after first whitespace (default: no)
- -sat [string]
-
specify kind of sequence representation by one of the keywords direct, bytecompress, eqlen, bit, uchar, ushort, uint32 (default: undefined)
- -dna [yes|no]
-
input is DNA sequence (default: no)
- -protein [yes|no]
-
input is protein sequence (default: no)
- -plain [yes|no]
-
process as plain text (default: no)
- -dust [yes|no]
-
mask low-complexity regions using the dust algorithm (default: no)
- -dustwindow [value]
-
windowsize for the dust algorithm (default: 64)
- -dustthreshold [value]
-
threshold for the dust algorithm (default: 2.000000)
- -dustlink [value]
-
Max. distance between regions masked by dust before merging. (default: 1)
- -indexname [string]
-
specify name for index to be generated (default: undefined)
- -smap [string]
-
specify file containing a symbol mapping (default: undefined)
- -lossless [yes|no]
-
allow lossless original sequence retrieval (default: no)
- -v [yes|no]
-
be verbose (default: no)
- -help
-
display help for basic options and exit
- -help+
-
display help for all options and exit
- -version
-
display version information and exit
REPORTING BUGS
Report bugs to https://github.com/genometools/genometools/issues.